Chaves (Mitchelton-Scott) put his climbing talents to the test in winning the 218km stage from Mitchelton Winery to Lake Mountain solo.
The Colombian was followed 42 seconds later by Australian Alexander Evans (Mobius Bridgelane) with Portuguese champion Ruben Guerreiro (Trek-Segafredo) leading the chasers through 27 seconds later.
The result turned over the general classification with Mitchelton-Scott now occupying the top three positions. Chaves is 32 seconds ahead of 2015 Tour winner Cameron Meyer and 39 seconds to reigning champion Damien Howson.
A host of riders are within striking distance of Chaves but it will be tough to overhaul the all Mitchelton-Scott trio now leading the general classification.
“I’m really happy to start the season with this form. It was a really hard tough race, nearly six hours on the bike," cHAVES SAID.
“We have a really strong team here and now finally we have a stage win and the jersey and this is really special for me.
“I made the move with 17 kilometres to go and it was a really long way but the plan was I try and if they bring me back then we have the other guys.
“It is beautiful in this team that everybody has a chance, everybody has an opportunity. The young fellas here are really strong.
“We are now top three overall and we need to enjoy this as winning bike races is not easy. Tomorrow is a hard one and people will attack for sure so we need to keep everything under control.”
A tough nine-lap 152km final stage set in and around Kinglake, which includes a 9km climb, will decide the outcome.
Full video highlights will be available online here at Cycling Central early on Sunday morning.